Purified MS2 replicase is functional in recombinant in vitro translation systems
To characterise the activity requirements of the MS2 replicase complex, we overexpressed the MS2rep subunit in E. coli and purified it by single-step immobilized metal ion affinity chromatography (IMAC). In the one-step purification protocol, MS2rep co-eluted with the two potential host factors ribosomal protein S1 and the translation factor (TF) EF-Ts, both of which are components of the related Qβ replicase complex (Supplementary Fig. 1). Surprisingly, we noticed that EF-Tu, which is an essential and tightly-binding host factor for the Qβ replicase complex that readily co-purifies with Qβrep, did not co-elute with the His-tagged MS2rep subunit. Thus, the assembly properties of the replicase core complexes between the genera Allolevivirus (Qβ) and Levivirus (MS2) show unexpected differences.
Next, we sought to explore if the MS2·S1·EF-Ts heterocomplex could be used to initiate transcription of a genuine MS2 template. To this end, we made use of our previously established MS2 RNA polymerase assay for the detection of MS2 replicase activity in recombinant in vitro transcription translation (PURE) systems (20, 28). In this assay, a fluorescence readout is produced by (+) strand synthesis of the broccoli aptamer from a (-) strand template that is fused with the 3’-end of genomic MS2 (-) strand (F30-Bro(-)), in the presence of the fluorogen DFHBI-1T (29) (Fig. 2A). In agreement with literature reports for in situ expressed MS2rep (20), we observed a strong fluorogenic readout when both F30-Bro(-) and MS2·S1·EF-Ts were incubated in the commercially available PURExpress® system. We also observed F30-Bro(+) synthesis, albeit at a lower level, in a homemade PURE system (PURE 3.0), which was prepared according to a previously established protocol (27) (Fig. 2B). Based on this result, we inferred that the PURE systems contained the host-factors required to assemble the active MS2 holoenzymes.
To further narrow down the range of possible E. coli proteins that are required for MS2 replicase activity, we investigated the activity in the presence of different PURE protein fractions. In PURE 3.0, 30 of the 31 E. coli TFs are obtained after co-expression and purification of the TF genes from three large expression plasmids resulting in three protein fractions (LD1, LD2 and LD3) (27). An additional enzyme mix contains 70S ribosomes as well as the elongation factor EF-Tu and the enzymes necessary to reconstitute a NTP regeneration system based on creatine phosphate (Supplementary Table 4). Initially, we tested MS2 replicase activity in reduced PURE 3.0 reactions (PUREred) based on the LD1-LD3 protein fractions. We also used a simplified enzyme mix containing only ribosomal protein S1 and EF-Tu because we did not expect that ribosomes or kinase enzymes to be the missing co-factors based on the genetic similarities between MS2 and Qβ (30). As anticipated, MS2 showed transcription of F30-Bro(+) in the PUREred environment (Fig. 2C). Next, we sought to narrow down the range of potential host factors by further omitting protein components from the PUREred setup. Hereby, we confirmed that TFs EF-Tu and the ribosomal protein S1 are critical co-factors required for full MS2 replicase activity, similarly to Qβ, as depletion of both proteins would lead to a drastic loss in F30-Bro(+) synthesis (Fig. 2C). While depletion of EF-Tu had a drastic effect on F30-Bro(+) synthesis, we still observed significant transcription in the absence of added S1 protein presumably due to the presence of S1 protein in the purified complex (Supplementary Fig. 1).
In addition to the expected dependency of the replicase on S1 and EF-Tu, we also observed an unforeseen impact on F30-Bro(+) synthesis upon depletion of the individual LD protein fractions. While depletion of both LD1 and LD3 appeared to weakly stimulate MS2rep activity, omission of LD2 caused a drastic loss of F30-Bro(+) transcription (Fig. 2C). LD2 contains eight enzymes, four tRNA synthetases (AlaRS, AsnRS, IleRS, PheRS1 + 2), E. coli Methionyl-tRNA formyltransferase (MTF), the translation elongation factor EF-Ts (which co-purifies with the MS2rep subunit), and the two translation initiation factors IF1 and IF3 (27). To identify TFs responsible for this marked effect on replicase activity, we performed selective depletion experiments with all LD2 proteins (Fig. 3A). Omitting the added EF-Ts led to a complete loss of activity, revealing that the excess amount of EF-Ts in the LD2 fractions is essential for transcription of the unnatural F30-Bro(-) template. We further observed an unexpected alteration of transcription activity by omitting the initiation factors IF1 and IF3. While depletion of IF1 caused a ~ 50% reduction in F30-Bro(+) synthesis, the omission of IF3 led to a more than 400% increase in transcription activity compared to the positive control reaction containing the full 1x LD2 protein fraction. These findings indicated that IF1 stimulates MS2 replicase activity, whereas IF3 acts as an inhibitor. This hypothesis was further corroborated in additional experiments, in which an excess of 5 µM of each of the eight individually purified LD2 proteins was added to the reaction mixture (Fig. 3B). Whereas excess IF1 led to an increased transcription activity, adding an excess of IF3 completely abolished F30-Bro(+) synthesis. In contrast, the omission or supplementation of the four tRNA synthetases had no impact on MS2 replicase activity. Both the inhibitory effect of IF3 and stimulating effect of IF1 showed clear dose-dependencies with observable effects already at low micromolar concentrations (Fig. 3C), supporting the notion that they are based on a direct functional interaction with the MS2 replicase core complex. In contrast, control experiments using MTF or PEG8000 at increasing concentrations showed that neither non-specific protein-protein interactions nor excluded volume effects are responsible for the observed modulation of replicase activity induced by IF1 and IF3. Furthermore, we found evidence that inhibition by IF3 is based on a direct competition between IF3 and the replicase for RNA binding as only an excess of the MS2rep complex could rescue transcriptional activity (Supplementary Fig. 2).
IF1 stimulates synthesis of the full-length MS2 genome
While the F30-Bro(+) synthesis enables monitoring (+) strand synthesis from an artificial (-) template, it provides no information on the complete replication cycle of the natural ~ 3600 nt MS2 genome. To probe full-length genome replication by the in vitro reconstituted MS2 replicase complex, we integrated the broccoli aptamer into the (+)-strand of MS2 wild type (MS2wt) genome at an amenable site downstream of the open reading frame for the maturation protein (MS2(+)Bro(+)) (Fig. 4A), where its insertion should only minimally interfere with replication (31–33). Using this construct, we were able to observe a continuous increase in DFHBI-1T fluorescence when the MS2rep·S1·EF-Ts complex was incubated in PURExpress system, which suggests processive genome replication (Fig. 4B). Comparison with reference inputs of MS2(+)Bro(+) showed an estimated sixfold amplification, corresponding to an increase of MS2(+)Bro(+) from 15 nM to approximately 90 nM over a 6-hour time course.
Having shown that the MS2 replicase complex can replicate genomic MS2 RNA in the PURExpress system, we further sought to dissect the influence of the individual co-factors on the ability of the replicase to synthesise the genomic (+) and (-) strands (Fig. 5A, B). Synthesis of genomic (+) and (-) strands from the corresponding MS2-Bro(-) template produced only a weak fluorescence output compared to synthesis of F30-Bro(+) from F30-Bro(-) template (Fig. 5C, D). Notably, the omission of an excess of S1 in these experiments did not significantly affect genome synthesis unlike for the shorter unnatural F30-bro construct used previously (Fig. 2). This finding indicates that the bound S1 present in the purified complex is sufficient for effective replication of the natural replicase substrate.
The fluorescence output of the broccoli aptamer domain during genomic (-) strand synthesis was seemingly not affected by supplementation of IF1 (Fig. 5E). At the same time, however, an in-gel fluorescence analysis revealed a drastic increase in RNA-synthesis in the presence of the co-factor, with the majority of product migrating at the expected size of a full-length duplex (Supplementary Fig. 3). This suggests that only very little newly synthesised (-) strand RNA was present as single strand. In contrast, a stimulation of both overall RNA synthesis as well as broccoli fluorescence was observed during synthesis of MS2(+)Bro(+) from MS2(‑)Bro(+) template in the presence of IF1 (Supplementary Fig. 3, Fig. 5F). Thus, IF1 stimulated MS2 replicase activity independent from the polarity of the template. In this minimal in vitro environment, the protein either caused a direct reduction of non-fluorescent inert duplex product during genomic (+) strand synthesis, or enhanced folding of the aptamer reporter domain.
Spontaneous formation of replicable RNA species
The purified replicase complex of phage Qβ is well known for its spontaneous in vitro synthesis of rapidly amplifying RNA species of different length and nucleotide sequence, even in the absence of externally added template molecules (34–36). To test if MS2rep is capable of a similar spontaneous generation of short amplifiable RNA species, we compared the activity of both purified Qβ and reconstituted MS2 core complex in template-free reactions supplemented with NTPs and SYBR Green nucleic acid stain. As expected, we observed a rapid increase in fluorescence after a brief lag phase of ~ 5–10 min in the presence of the Qβ heterotetramer (Fig. 6A), suggestive of the rapid formation of small amplifying RNA species (“RNA parasites”) described in previous studies (36). We verified the efficient formation of small replicable RNAs by the Qβ replicase by gel electrophoresis (Supplementary Fig. 4). Surprisingly, we observed no such spontaneous formation of RNAs when the MS2 replicase complex in the presence of IF1 was incubated for 75 min under the same conditions (Fig. 6A). As the MS2 enzyme did not show a similar strong background activity as the Qβ core complex, we asked whether the enzyme was able to produce short amplifying RNAs as by-products during MS2 genome replication. To test this hypothesis, we performed serial transfer experiments with the MS2 replicase core complex (MS2rep·S1·EF-Ts·EF-Tu) in the absence and presence of IF1 and MS2(+) RNA (Fig. 6B). In reactions with the full-length genome, we observed a rapid degeneration of the ~ 3600 nt RNA molecule during the first two dilutions concomitant with the emergence of smaller RNA species with a broad size distribution and a dominant RNA band migrating at ~ 200 nt. The emergence of aberrant RNA products was strongly increased when the MS2 core complex was further supplemented with IF1. Intriguingly, in the presence of IF1, the small RNA species emerged even in the absence of input MS2(+) after the first serial transfer (Fig. 6B). To obtain more information about the sequence properties of the newly evolved RNA replicators, we reverse transcribed, sequenced, and analysed the reaction products. Notably, we obtained only a single clonal sequence from these experiments (MSRP-22), which showed an almost perfect homology with the first 118 nt of the 5’UTR and 105 nt of the 3’ UTR of MS2wt (Fig. 7A, B, Supplementary Table 5). We confirmed that MSRP-22 is a genuine RNA template for MS2 replicase since it was specifically amplified in an input concentrations-dependent manner in batch reactions (Fig. 7C). In contrast, MS2rep was not able to amplify RQ135, a typical RNA parasite of Qβrep (37) within the same time window. This finding confirmed the differential template requirements of both phage replicases.